Additional file 1.

Marker typing results according to stages. Summary of marker typing results for the initial (“First”) set of HAPPY markers, for redesigned markers (“Second” and “Third”), for markers designed against chromosomally-assigned genes (“Chr”), and for all markers combined ("Overall"). Based on the average DNA content of each aliquot in the mapping panel, and on the Poisson distribution, we expect a single-copy sequence to be represented in 30-55 of the aliquots (mean ±2 s.d.); markers in this range are classified as good (green). Markers giving <30 positives, probably due to poor amplification, are classified as low copy (yellow), whilst those giving >55 positives are presumed to represent multi-copy sequences (blue). Markers that did not amplify are considered failed (red).

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Lim et al. BMC Genomics 2012 13:389   doi:10.1186/1471-2164-13-389